Bioenergetic defects secondary to mitochondrial dysfunction occur in many severe illnesses, but the mechanisms by which mitochondria respond to, or accommodate the damage are not well understood. Very recently it has been demonstrated that survival in septic patients can be predicted by the strength of their mitochondrial biogenic response. Hypoxia, which complicates many cardiopulmonary, infectious, and neoplastic disorders, is one of multiple stimuli causing mitochondrial biogenesis. The mechanism underlying this adaptive response is unknown, but it is important that many stimuli known to increase mitochondrial biogenesis use reactive oxygen species (ROS) as second messengers. The proposed research will explore, at molecular and functional levels, a novel pathway regulating mitochondrial biogenesis. Traditional concepts hold that maintenance of DNA integrity is required for proper cell function. However, there is emerging evidence that, at least for nuclear genes, controlled DNA damage and repair may be necessary for normal transcriptional regulation. In lung vascular cells, for example, hypoxia causes ROS- dependent base modifications within hypoxic response elements (HREs) of hypoxia inducible genes. Because the lesions are restricted to HREs associated with transcriptionally-active nucleosomes and since mimicking the effect of hypoxia by introducing modified bases in the HRE of the VEGF promoter leads to enhanced DNA flexibility, altered transcription complex assembly and more robust reporter gene expression, it has been proposed that ROS-mediated DNA damage and repair may serve to alter the topology of key DNA sequences to enable regulatory protein binding and facilitate transcription. We propose to test the hypothesis that controlled oxidative DNA damage and repair in the D-loop region facilitates mtDNA transcription and replication. Using established strategies to alter the mtDNA repair efficiency, we will: (1) test the hypothesis that manipulation of hypoxia-induced oxidative damage to the mtDNA D-loop region coordinately regulates mtDNA replication and transcription in hypoxia, and, (2) determine whether formation and repair of hypoxia-caused oxidative base modifications in the D-loop region are required for transcription factor binding. If the concept that controlled DNA damage and repair govern mtDNA transcription and replication in hypoxia is valid, it will represent a significant advance in understanding how mitochondrial gene expression is regulated in health and diseases, including a number of disorders in which hypoxia and mitochondrial dysfunction have been incriminated. It will also contribute to a more detailed appreciation of the link between oxidant signaling and pathways governing mitochondrial adaptation, and thus point to new strategies for correcting mitochondrial bioenergetic defects in many disorders with such abnormalities.